Did you go thought the entire activity setup wizard? though this wizard, there are very detailed screens that ask questions about how to enter in one/two/three digit channels. I have three TV's in the house and each do it a little differently -- this remote handles each one perfectly and I can use the TV guide for each TV.
Try going through the activity setup again an answer all of the questions. Let me know if you get a different result.
Universal Remote: Sony AV-RM3100, TV - Samsung TXJ2766, AMP - Sony STR-DE845, DVD - Sony DVP-3000, Tape - Sony TC-WE435, VCR - Panasonic PV-8661